As Alaska Airlines gets down to finalizing its merger with Virgin America, some changes are hitting travelers close to home: in their mileage accounts. While not unexpected, the news that Alaska and Delta Air Lines will all but sever their longstanding ties as of April 30 is shaking things up—in part because they had such an unusually wide-ranging deal for two U.S. airlines.

Among other things, Alaska and Delta have a codeshare agreement that puts each other's two-letter code on dozens of flights, plus a mileage redemption arrangement. They also provide reciprocal benefits for elite fliers, meaning that Alaska’s top customers, for example, are eligible for perks like free upgrades and preferred boarding on Delta, and vice versa. The practical effect of the breakup, then, is that Delta fliers won’t be able to redeem their miles for an Alaska-operated flight, and presumably, Alaska high-milers can’t do the same on Delta. Alaska is also scaling back its code-sharing alliance with American, which was a condition of the Justice Department’s approval of the Virgin merger. It won’t shut down entirely, however, and fliers will still see some reciprocal benefits in their mileage accounts.

The shuffle is partly a reflection of the fact that Alaska relied on partnerships with major U.S. international airlines to feed traffic to its mostly domestic network. Delta in particular had been a strong partner in that regard after it opened a transpacific hub in Seattle, offering a number of long-haul flights to Asia that fit well with Alaska’s strong presence there. But their relations cooled considerably after Delta decided to boost its domestic flights from Seattle and started directly competing with its erstwhile partner.

Alaska is putting a positive spin on the moves as it sweetens some benefits for frequent fliers, such as lowering the miles needed to redeem some award flights; it’s moving swiftly to align its mileage program with Virgin America’s Elevate. Meanwhile, Virgin partners such as the Starwood hotel group (which just minted its own merger with Marriott) are already moving to switch their allegiance to Alaska, according to the Points Guy. Alaska says that as of January 9, Elevate members will be invited to join its mileage plan and can convert their miles to Alaska's at a 1:1.3 ratio, with their status matched.

But some industry experts said the changes won’t necessarily be good for all.

“The end of the Delta-Alaska codesharing partnership means less choice for consumers,” said Henry Harteveldt, founder and head of the Atmosphere Research Group, a research and advisory firm focused on travel. He noted that previously, an Alaska frequent flier had the choice of whether to credit loyalty points to Alaska's, American’s, or Delta’s loyalty programs, and Delta’s SkyMiles members could choose to credit miles flown to Alaska or Delta. Now, Alaska members can choose only between Alaska and American, and Delta members lose the Alaska affiliation completely, he said.

The other big question looming is what will happen to the Virgin America brand. Alaska Airlines has said that the Virgin colors will continue to fly on that carriers’ fleet of A320s, in contrast to Alaska’s larger fleet of Boeing 737s, which bear its distinctive Eskimo logo. But operating two distinct fleet types and two brands is not only costly but it risks stoking consumer confusion, observers note. “I strongly suspect the Virgin America brand will disappear, “ Harteveldt said. “The two airlines have different on-board products and different policies that affect travelers, and maintaining the two airlines may also lead to labor problems,” he added, noting that when other airlines have tried to maintain separate identities in a merged company, “it didn’t end well.” Still, he said, “it will be sad to see the Virgin America name fade away,” but “it makes good business sense to consolidate under the Alaska brand name."